The term "chimera" has come to describe any mythical or fictional creature with parts taken from various animals, to describe anything composed of disparate parts or perceived as wildly imaginative, implausible, or dazzling. In other words, a chimera can be any hybrid creature.

According to Hesiod, the Chimera's mother was a certain ambiguous "she", which may refer to Echidna, in which case the father would presumably be Typhon, though possibly (unlikely) the Hydra or even Ceto was meant instead.[4] However, the mythographers Apollodorus (citing Hesiod as his source) and Hyginus both make the Chimera the offspring of Echidna and Typhon.[5] Hesiod also has the Sphinx and the Nemean lion as the offspring of Orthus, and another ambiguous "she", often understood as probably referring to the Chimera, although possibly instead to Echidna, or again even Ceto.[6]

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Homer described the Chimera in the Iliad, saying that "she was of divine stock not of men, in the fore part a lion, in the hinder a serpent, and in the midst a goat, breathing forth in terrible wise the might of blazing fire."[7] Hesiod and Apollodorus gave similar descriptions: a three-headed creature with a lion in front, a fire-breathing goat in the middle, and a serpent in the rear.[8]

According to Homer, the Chimera, who was reared by Araisodarus (the father of Atymnius and Maris, Trojan warriors killed by Nestor's sons Antilochus and Trasymedes), was "a bane to many men".[9] As told in the Iliad, the hero Bellerophon was ordered by the king of Lycia to slay the Chimera (hoping the monster would kill Bellerophon). Still, the hero, "trusting in the signs of the gods", succeeded in killing the Chimera.[10] Hesiod adds that Bellerophon had help in killing the Chimera, saying, "her did Pegasus and noble Bellerophon slay".[11]

Apollodorus gave a more complete account of the story. Iobates, the king of Lycia, had ordered Bellerophon to kill the Chimera (who had been killing cattle and had "devastated the country") since he thought that the Chimera would instead kill Bellerophon, "for it was more than a match for many, let alone one".[12] But the hero mounted his winged horse Pegasus (which had sprung from the blood of the Medusa)[13] "and soaring on high shot down the Chimera from the height."[14]

Although the Chimera was, according to Homer, situated in foreign Lycia,[15] her representation in the arts was wholly Greek.[16] An autonomous tradition that did not rely on the written word was represented in the visual repertory of the Greek vase painters. The Chimera first appeared early in the repertory of the proto-Corinthian pottery painters, providing some of the earliest identifiable mythological scenes that may be recognized in Greek art. After some early hesitation, the Corinthian type was fixed in the 670s BC; the variations in the pictorial representations suggest multiple origins to Marilyn Low Schmitt.[17] The fascination with the monstrous devolved by the end of the seventh century into a decorative Chimera motif in Corinth,[18] while the motif of Bellerophon on Pegasus took on a separate existence alone. A separate Attic tradition, where the goats breathe fire and the animal's rear is serpentine, begins with the confidence that Marilyn Low Schmitt is convinced that there must be unrecognized or undiscovered local precursors.[19] Two vase painters employed the motif so consistently they were given the pseudonyms the Bellerophon Painter and the Chimaera Painter.

A fire-breathing lioness was one of the earliest solar and war deities in Ancient Egypt (representations from 3000 years prior to the Greeks), and influences are feasible. The lioness represented the war goddess and protector of both cultures that would unite as Ancient Egypt. Sekhmet was one of the dominant deities in upper Egypt and Bast in lower Egypt. As the divine mother, and more especially as protector, for Lower Egypt, Bast became strongly associated with Wadjet, the patron goddess of Lower Egypt.[citation needed]

In Etruscan civilization, the Chimera appears in the Orientalizing period that precedes Etruscan Archaic art. The Chimera appears in Etruscan wall paintings of the fourth century BC.[citation needed]

In Indus civilization are pictures of the Chimera in many seals. There are different kinds of Chimera composed of animals from the Indian subcontinent. It is not known what the Indus people called the Chimera. [citation needed]

Pliny the Elder cited Ctesias and quoted Photius identifying the Chimera with an area of permanent gas vents that still may be found by hikers on the Lycian Way in southwest Turkey. Called in Turkish, Yanarta (flaming rock), the area contains some two dozen vents in the ground, grouped in two patches on the hillside above the Temple of Hephaestus approximately 3 km north of ral, near ancient Olympos, in Lycia. The vents emit burning methane thought to be of metamorphic origin. The fires of these were landmarks in ancient times and were used for navigation by sailors.

I have used Dada2 for the denoising step. As I know Dada2 also includes removing chimera. I am wondering that it is necessary to remove chimera with qiime vsearch uchime-denovo after denosing by Dada2 or not?

Recently, I have read the workflow of Qiime 2 I recognize that Denoise with Dada2 will generate the ASVs. Therefore, I am wondering if I like to get OTUs, it is necessary to do denoise with Dada2 or not. In case I do not use denoising with Dada2, do I need to perform other steps to remove and/or correct noisy reads and chimera? As you mentioned if I use Dada2, I do not need to do removing chimera. However, if I do not run Dada2 I still have to do removing chimera with vsearch uchime-denovo, is that right?

these files are analogous to those generated by qiime dada2 denoise-* and qiime deblur , except that no denoising, chimera removal, or other quality control has been applied in the dereplication process."

Taking this approach probably means manually applying your own QC, as you've suggested. By correcting rather than dropping or ignoring noisy reads, DADA2 provides the added benefit of reducing the number of false positives, often apparently yielding fewer ASVs than you would have gotten OTUs from clustering methods.

What you choose for your analysis should fit your study needs, but as a side note, here's an amazing, brief look at the history of taxonomic assignment and clustering, with additional good posts linked in it. Depending on your specific work, you may be able to simplify your pipeline and preserve more data without clustering to 97%. There are definitely cases where clustering/OTU picking avoids pitfalls inherent to ASV/denoising methods, but it's worth a read if you haven't considered this approach.

Thank you for sharing ideas. Indeed, it is helpful.

I have recently read the tutorial " Clustering sequences into OTUs using q2-vsearch" . It mentions it is possible to do clustering after running denoising with Dada2 or Deblur if I understand well from the tutorial . You can see below

Clustering of sequences or features into OTUs using vsearch is currently possible from demultiplexed, quality-controlled sequence data (i.e., a SampleData[Sequences] artifact), or from dereplicated, quality-controlled data in feature table and feature representative sequences (i.e., the FeatureTable[Frequency] and FeatureData[Sequence] artifacts, which could be generated using the qiime dada2 denoise-* or qiime deblur denoise-* commands).

I agree with you that ASVs (99% ) generated from Dada 2 is fewer than OTUs (97%) from clustering methods. Indeed, 97% is a common similarity threshold because studies showed that most strains had 97% 16S rRNA sequence similarity. However, many criticisms regarding using percent sequence similarity to define OTUs. I am wondering if we use Dada2, can we generate ASVs with 97% similarity?

@Tintin, I think I've done all I can here. If you're asking whether it's OK to denoise then cluster, I think the tutorial points pretty clearly toward "Yes." If you're asking a deeper bioinformatics question, unfortunately it's beyond my expertise to answer, or even understand.

In my understanding, these are not 99% OTUs, but rather exact sequences, with differences resolved to the single-nucleotide level. There is no clustering, any reduction in counts is not a byproduct of clustering (with associated loss of information), but by correcting "noise" - artificial variance in the sequence introduced during prep/sequencing/whatever. Ben Callahan treats the concepts well in greater detail in this preprint.

My sequence data is pre-quality checked so I dont use DADA2 or Deblur at this point. Where would I insert the chimera checking step into the pipeline? Any preference of which uchime method to use given my workflow?

Uchime-denovo requires size annotations, so you have to run it after step 1 (dereplication adds size annotations). I have seen people do uchime-denovo before or after clustering (or both!). Greg recommends running it after clustering.

Obviously, chimera check retains too many sequences with the default configuration. So, I have 2 questions: What could be a reason why I have so many declared chimeric sequences based on default? What parameters (--p-dn FLOAT,--p-mindiffs INTEGER RANGE,--p-mindiv FLOAT,--p-minh FLOAT,--p-xn FLOAT) can I tweak to soften the chimera-filtering and retain a higher proportion of my sequences?

Is there any recommendation for which database to use for uchime-ref for 16S primers targeting bacteria and archaea. In the literature I have seen the Silva Gold database (used by chimera slayer) and a database by the Broad Institute as part of their Microbiome Utilities package.

You could also use the full database you use for taxonomy assignment. The developer of uchime used to recommend small, high-quality databases. Then he recommended large, complete databases. Now he recommends using a de novo filter based on your current data set (something like uchime-denovo). 152ee80cbc

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